his_emr_api_lab 0.0.6 → 0.0.11

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 060337303a9a04fc0f9cebbe525f2275964b41776297b440bc9d7ea4c25c39b8
+  data.tar.gz: 5cc5383ab62d941de6a0d5fa2f51c5199461f141459cea072b40c004277855d1
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+  metadata.gz: 25e70f8e501dd0f0edf25b6f202f41129842fe5099cd5e6d977035df063d9233ac38b98e51ebdd2c2bcb382524da111b42138815d0a48c02e5bdb979b43c8127
+  data.tar.gz: 950d9d988b026ac2dbaed9f63be620cc474816aaba77c64231291e721e463f2872a20c2f629a553d1c52c0689e20afb28d44fa1c981807e1a0c4ed7945d6103f

data/app/services/lab/labelling_service/order_label.rb

@@ -27,7 +27,7 @@ module Lab
                                '',
                                drawer,
                                '',
-                               specimen,
+                               tests,
                                reason_for_test,
                                order.accession_number,
                                order.accession_number)
@@ -36,7 +36,7 @@ module Lab
       def reason_for_test
         return 'Unknown' unless order.reason_for_test
 
-        ConceptName.find_by_concept_id(order.reason_for_test.value_coded)&.name || 'Unknown'
+        short_concept_name(order.reason_for_test.value_coded) || 'Unknown'
       end
 
       def patient
@@ -60,11 +60,14 @@ module Lab
       def drawer
         return 'N/A' if order.concept_id == unknown_concept.concept_id
 
-        name = PersonName.find_by_person_id(order.creator)
-        return "#{name.given_name} #{name.family_name}" if name
+        drawer_id = order.discontinued_by || order.creator
+        draw_date = (order.discontinued_date || order.start_date).strftime('%d/%^b/%Y %H:%M:%S')
 
-        user = User.find(order.creator)
-        user&.username || 'N/A'
+        name = PersonName.find_by_person_id(drawer_id)
+        return "#{name.given_name} #{name.family_name} #{draw_date}" if name
+
+        user = User.find_by_user_id(drawer_id)
+        user ? "#{user.username} #{draw_date}" : 'N/A'
       end
 
       def specimen
@@ -73,6 +76,24 @@ module Lab
         ConceptName.find_by_concept_id(order.concept_id)&.name || 'Unknown'
       end
 
+      def tests
+        tests = order.tests.map do |test|
+          name = short_concept_name(test.value_coded) || 'Unknown'
+
+          next 'VL' if name.match?(/Viral load/i)
+
+          name.size > 7 ? name[0..6] : name
+        end
+
+        tests.join(', ')
+      end
+
+      def short_concept_name(concept_id)
+        ConceptName.where(concept_id: concept_id)
+                   .min_by { |concept| concept.name.size }
+                   &.name
+      end
+
       def unknown_concept
         ConceptName.find_by_name('Unknown')
       end

data/app/services/lab/lims/migrator.rb

@@ -142,9 +142,10 @@ module Lab
       MIGRATION_REJECTIONS_CSV_PATH = LIMS_LOG_PATH.join('migration-rejections.csv')
 
       def self.export_rejections(rejections)
-        headers = ['Accession number', 'NHID', 'First name', 'Last name', 'Reason']
+        headers = ['doc_id', 'Accession number', 'NHID', 'First name', 'Last name', 'Reason']
         rows = (rejections || []).map do |rejection|
           [
+            rejection.order[:_id],
             rejection.order[:tracking_number],
             rejection.order[:patient][:id],
             rejection.order[:patient][:first_name],
@@ -159,9 +160,10 @@ module Lab
       MIGRATION_FAILURES_CSV_PATH = LIMS_LOG_PATH.join('migration-failures.csv')
 
       def self.export_failures
-        headers = ['Accession number', 'NHID', 'Reason', 'Difference']
+        headers = ['doc_id', 'Accession number', 'NHID', 'Reason', 'Difference']
         rows = Lab::LimsFailedImport.all.map do |failure|
           [
+            failure.lims_id,
             failure.tracking_number,
             failure.patient_nhid,
             failure.reason,

data/app/services/lab/lims/order_dto.rb

@@ -30,9 +30,9 @@ module Lab
 
       # Translates a LIMS specimen name to an OpenMRS concept_id
       def specimen_type_id
-        lims_specimen_name = self['sample_type']
+        lims_specimen_name = self['sample_type']&.strip&.downcase
 
-        if %w[specimen_not_collected not_assigned].include?(lims_specimen_name)
+        if %w[specimen_not_collected not_assigned not_specified].include?(lims_specimen_name)
           return ConceptName.select(:concept_id).find_by_name!('Unknown').concept_id
         end
 
@@ -53,6 +53,8 @@ module Lab
 
       # Extract requesting clinician name from LIMS
       def requesting_clinician
+        return 'Unknown' unless self['who_order_test']
+
         # TODO: Extend requesting clinician to an obs tree having extra parameters
         # like phone number and ID to closely match the lims user.
         first_name = self['who_order_test']['first_name'] || ''
@@ -67,6 +69,10 @@ module Lab
       end
 
       def start_date
+        if self['date_created'].blank?
+          raise LimsException, 'Order missing created date'
+        end
+
         Utils.parse_date(self['date_created'])
       end
 

data/app/services/lab/lims/utils.rb

@@ -66,6 +66,8 @@ module Lab
           Date.strptime(str_date, '%d-%m-%Y').strftime('%Y-%m-%d')
         elsif str_date.match?(/(\d{4}\d{2}\d{2})\d+/)
           Date.strptime(str_date, '%Y%m%d').strftime('%Y-%m-%d')
+        elsif str_date.match?(%r{\d{2}/\d{2}/\d{4}})
+          str_date.to_date.to_s
         else
           Rails.logger.warn("Invalid date: #{str_date}")
           parse_date(fallback_date)

data/app/services/lab/lims/worker.rb

@@ -28,7 +28,9 @@ module Lab
           fout.write("Worker ##{Process.pid} started at #{Time.now}")
           worker = new(Api.new)
           worker.pull_orders
-          worker.push_orders
+          # TODO: Verify that names being pushed to LIMS are of the correct format (ie matching
+          # LIMS naming conventions). Enable pushing when that is done
+          # worker.push_orders
         end
       end
 

data/lib/lab/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Lab
-  VERSION = '0.0.6'
+  VERSION = '0.0.11'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: his_emr_api_lab
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.11
 platform: ruby
 authors:
 - Elizabeth Glaser Pediatric Foundation Malawi
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-23 00:00:00.000000000 Z
+date: 2021-04-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: couchrest